The invention relates to the fragmentation of parent ions in ion traps filled with collision gas by exciting their axial oscillations in a dipolar excitation field with a frequency mixture which covers the oscillation frequencies of the parent ions.
The invention consists of ramping up the voltages of the frequency mixture for the dipolar excitation field, resulting in, surprisingly, approximately the same fragmentation in the same fragmentation times as with optimal voltage applied at a constant level, even for parent ions of different structures needing structurally specific fragmentation voltages.
Fragmentation of ions is necessary if daughter ion spectra have to be acquired. Daughter ions are nothing but charged fragments of the parent ions which result from them due to disintegration when energy is supplied into the ions.
The supplied energy can be radiation energy for instance; a new method here is BIRD=xe2x80x9cBlackbody Infrared Radiation Dissociationxe2x80x9d, which, however, only works in the case of large molecular ions and requires a considerable amount of apparatus. Generally the energy can be much more simply introduced to the ions by impact with a collision gas (abbreviated to CID=xe2x80x9cCollisionally Induced Dissociationxe2x80x9d; sometimes also called CAD=xe2x80x9cCollisionally Activated Dissociationxe2x80x9d).
Between two mass spectrometers arranged in series at a distance from each other one can shoot the ions through a cell containing collision gas between the spectrometers at relatively high levels of energy and then individual collisions already lead to spontaneous fragmentation. The daughter ions only lose a small amount of velocity; they can be fragmented into granddaughter ions in the same cell by another impact, and so on; these high-energy daughter ion spectra appear very different from low-energy daughter ion spectra due to the large number of descendant fragment ions.
In ion traps the ions cannot be accelerated such that an individual impact is sufficient for a fragmentation. By exciting the oscillations in the quasi potential well internal energy must be collected from a large number of low energy impacts until the ion ultimately breaks. Fractures are no longer spontaneous: the collected energy is statistically distributed over the entire ion, over all the possible oscillation states of the inner structure, and drifts to and fro inside of the ion due to coupled oscillations, until, due to random superimposition, a bond with low bonding energy collects sufficient energy for fracture.
The daughter ions have a different mass and thus a different oscillation frequency in the ion trap so they are no longer excited by the excitation frequency; on the contrary, they are cooled and decelerated by further impacts in the collision gas. Consequently, further granddaughter ions are not formed immediately; the spectra are pure daughter ion spectra.
Scanning granddaughter ion spectra calls for a two-stage fragmentation process: generation of initial substance ions, isolation of the selected parent ion type, fragmentation to form daughter ions, isolation of a selected daughter ion type, fragmentation to form granddaughter ions, and scanning the granddaughter ion spectrum. At the beginning of the process the ion trap has to be filled with sufficient ions - overloading generally causes no damage. Scanning great granddaughter spectra requires another intermediate step of isolation and fragmentation. Further descendant spectra can be scanned, the only prerequisite being that at the start the ion trap contains sufficient initial ions of the substance. The necessary filling can, from a series of spectra, be calculated by the method described in GB 2 322 961 (U.S. Pat. No. 5,936,241) and controlled. Commercially available ion traps permit generation of descendant spectra up to the tenth generation and above.
These non spontaneous fractures of the ions in ion traps are particularly informative about their structure because, firstly, they clearly relate to the bonds with the lowest levels of bonding energy and, secondly, because they indicate the relationship between the daughter and the mother. In high-energy impacts the relationship between the great granddaughter and the granddaughter, and also between the daughter and the mother, can no longer be read off in a simple manner. Only by complex methods of marking with enriched isotopes can the path of fraction and therefore the possible structure of the ion be clearly described.
Measurement of all the main daughter, granddaughter, and great granddaughter spectra in an ion trap therefore ideally reflects the fragmentation path and is of inestimable value in determining the structure and identity of the initial ion. Automatic measurement of all these ion spectra is desirable, but at the moment it is not practicable. It would be optimal if this automatic measurement could also be performed in the short time which is available in a separation of substances of a mixture, by liquid chromatography, for example, i.e. in about ten seconds.
The quantity of energy for fragmentation is, however, dependent on the structure of the ions. There are ion structures which already allow fragmentation by minimal energy imparted, and other ones which require much more energy. The optimal excitation voltage of an easily fragmentable ion and a poorly fragmentable ion of the same mass may well differ by a factor of 6. The optimum of the best excitation voltage is relatively sharp: slightly too little or too much voltage may even cause no fragmentation orxe2x80x94for reasons which are not fully understood yet no collectable daughter ions, possibly because the parent ions hit the end cap electrodes of the ion trap prior to their fragmentation.
Automation of the scanning of daughter spectra (and granddaughter spectra) in ion traps therefore becomes practically impossible, or at least exceptionally difficult. Graduated trial and error to achieve optimal fragmentation voltage is usually impossible because there is insufficient time.
Even within a group of similar substancesxe2x80x94as for example the peptidesxe2x80x94optimal fragmentation of the ions is still considerably dependent on the (usually still unknown) composition and structure of the ions. In addition, there is also an increase in the optimal excitation voltage as the mass of the ions increases, which superimposes itself on the structural difference. It can be explained by the fact that the energy is distributed over more degrees of freedom if the molecular ion is larger.
Moreover, the energy has to be supplied in a short time period because as the collected energy increases it is emitted by radiation or dissipated by very low-energy collisions (in the thermal range). Dissipation by radiation has a fixed time constant so the energy absorbed can only take on satisfactorily high levels if the supply of energy takes place within a short period of time. Before the ions of an ion type are fragmented, all the other ions which are in the ion trap are ejected from the trap by a special process so that these ions do not superimpose the spectrum of the daughter ions. This process is called isolation: only the ions to be fragmented are left in the ion trap. Since doubly charged parent ions can also form daughter ions whose mass-to-charge ratio m/e is larger than that of the parent ions, the ions not of interest which are heavier than the parent ions must also be removed, whereby the term xe2x80x9cheavierxe2x80x9d (as also the term xe2x80x9clighterxe2x80x9d used in the following) relates to the mass-to-charge ratio m/e.
Scanning daughter ion spectra has proved particularly successful for investigating peptides in ionization by the electrospray method. The peptides usually stem from a digest of a larger protein due to an enzyme, trypsin for example. These digest peptides cover a mass range m of approx. 500 to approx. 4,000 atomic mass units. However, not only singly charged ions are generated but also ones with two, three, and even four charges. As a general rule of thumb one can say that the center of charge distribution increases by one charge per thousand mass units.
In ion traps it has been particularly useful to apply the doubly charged ions for fragmentation. There are several reasons for this, one of which being the easier fragmentability. However, especially the span between the smallest detectable daughter ion, given by the separation limit ma/e of the ion traps for light ions, and the largest daughter ion (relative to m/e) is much larger than for singly charged parent ions.
In practice it has proved favorable to not isolate the ions monoisotopically but to leave all the ions of a mass-to-charge ratio with the isotopic companions inside of the ion trap and to fragment them together. This produces the advantage that it is possible to immediately see from the distance between the isotopic peaks whether the daughter ions have one or several charges. Joint fragmentation of all isotopic masses, however, means it is essential to use a frequency mixture for fragmentation. The mixture must cover the frequencies of the ions involved. This might be most simply achieved if for each of the involved ionic types of the same isotopic mass a separate fragmentation frequency were calculated and applied.
Unfortunately the construction of modem ion traps, which necessitates a so-called nonlinear ion trap geometry with superimposition of higher multipole fields for physical reasons which will not be explained here, does not permit a separate fragmentation frequency for each isotopic peak. The oscillation frequency of the ions changes due to the nonlinear field components with increasing oscillation amplitude. Excitation of the ions must therefore xe2x80x9cswitch overxe2x80x9d from an initially effective excitation frequency with oscillation amplitude increasing to an adjacent frequency. This switchover in turn only succeeds if the two adjacent excitation frequencies are in phase.
A frequency mixture can only consists of individual discrete frequencies with a discrete frequency spacing. The smaller the frequency spacing, the longer it takes for two adjacent frequencies to come into phase, without which the switchover is not possible. In other words, at a frequency spacing of 250 hertz between two adjacent frequencies the frequencies are in phase exactly every four milliseconds. Consequently, a switchover is possible every four milliseconds. If the spacing is closer at 100 hertz, the switchover is only possible every ten milliseconds. Fragmentation with a frequency mixture is known from GB 2 291 534 (U.S. Pat. No. 5,528,031). The problems of switching to adjacent frequencies are explained in GB 2 297 192 (U.S. Pat. No. 5,654,542).
The fragmentation must take place in such a way that the daughter ions, the masses of which are always lighter than those of the parent ions, can be collected in the trap. Fragmentation must therefore be performed at an RF amplitude which is far away from the amplitude for the lower threshold limit for ion storage. Generally three times the amplitude value for the threshold old limit ma/e is used, i.e. all the daughter ions the m/e of which is between one third and the full m/e of the parent ions, can be collected in the ion trap and measured as a spectrum. On account of the RF amplitude the oscillation frequency of the parent ions and therefore the excitation frequency is determined for their fragmentation. A favorable value for fragmentation in an ion trap, which operates at a thrust frequency of approx. 800 kilohertz, is, for example, 75 kilohertz. If for ions with a mass of 1,000 atomic mass units fragmentation is to detect about 10 masses, the mixture must have a frequency width of about 750 hertz.
At a mass of 1,000 atomic mass units an isotope group has about four measurable isotopic lines at 1,000, 1,001, 1,002, and 1,003 atomic mass units. If there is an increase in the amplitude of their oscillations in the z direction, the ions change their oscillation frequency by an amount which corresponds to approx. two to three mass units. If one also takes into consideration the accuracy of calibration, one arrives at a desirable width of excitation amounting to approx. 10 mass units.
An optimal fragmentation consists in fragmenting about 80% to 100% of the parent ions in as short a time as possible. It turns out that for this purpose the application of four frequencies with three spacings each of 250 hertz is more favorable than the application of eight frequencies, for example, with seven spacings each of 100 hertz, which probably has to do with the above-mentioned switchovers. Although the isotope frequency is slightly distorted during fragmentation, the time required for optimal fragmentation is much shorter. Assuming that the excitation amplitude is set optimally, fragmentation takes only about 40 milliseconds, so it permits about ten switches to an adjacent frequency. At a frequency spacing of only 100 hertz, only four switches would be possible in the 40 milliseconds; but a larger number of switches would be necessary due to the smaller frequency spacing.
It is the objective of the invention to find a method which, without extending fragmentation time, makes it possible to fragment as optimally as possible ions with very different structures without having any prior knowledge of the most favorable voltage exciting the ions for fragmentation.
The invention consists of applying the fragmentation amplitude of the axially exciting voltage not constantly over the entire fragmentation time at an optimal value but ramping that fragmentation amplitude from small values to large values without extending the usual fragmentation time. One variant consists of selecting quite a high fragmentation amplitude, initially for a very short time, and then scanning the fragmentation voltage from small values to large values.
Surprisingly it has been established that a ramp in fragmentation amplitude which commences at about one third of the average value of the fragmentation amplitude for ions of this mass and runs up to double the average value in the customary fragmentation time, simultaneously achieves very good fragmentation results for ions with very different structures. The fragmentation yields are only slightly below those which are found for an optimal, constantly applied fragmentation amplitude. It is not yet understood why this ramp, which for each individual ionic type provides the optimal amplitude only for a very short time, produces such favorable results. For different groups of analytes, such as peptides or artificial polymers, the optimum range of ramping may be lower or higher than given above; the ramping may increase the initial voltage by factors between two and ten.
The ramp may be increased linearly or exponentially. Other ramp shapes, for example, compounded from a number of linear rises, can also be selected.
Initial and ultimate values of the ramp can be selected to be dependent on the mass and charge of the ions, according to the dependence of the average fragmentation amplitude on the mass or charge.
For ions of known structure families, e.g. peptides, ramps can be specially configured, for example, by restricting the extent of the ramp or by creating special ramp shapes.